Variant report

Variant	rs77279256
Chromosome Location	chr1:47902672-47902673
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:47901943-47902736	HCT-116	colon:	n/a	chr1:47902581-47902591 chr1:47902581-47902593
2	MTA3	chr1:47901994-47902922	GM12878	blood:	n/a	n/a
3	MXI1	chr1:47902143-47902673	HepG2	liver:	n/a	chr1:47902655-47902670
4	POLR2A	chr1:47902127-47903588	GM12878	blood:	n/a	n/a
5	CTCF	chr1:47901969-47903966	A549	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
6	CTCF	chr1:47902083-47903846	IMR90	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
7	TCF7L2	chr1:47902190-47903850	HCT-116	colon:	n/a	n/a
8	CTCF	chr1:47902547-47902677	H1-hESC	embryonic stem cell:	n/a	chr1:47902578-47902591
9	ELF1	chr1:47902073-47903938	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
10	RCOR1	chr1:47901790-47903838	K562	blood:	n/a	n/a
11	UBTF	chr1:47902126-47904027	K562	blood:	n/a	n/a
12	ZBTB7A	chr1:47902143-47904182	K562	blood:	n/a	chr1:47903645-47903654
13	MAX	chr1:47902072-47903880	NB4	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
14	NR2F2	chr1:47902020-47902814	K562	blood:	n/a	n/a
15	POLR2A	chr1:47902034-47904062	HEK293	kidney:	n/a	n/a
16	CTCF	chr1:47902660-47902810	GM12872	blood:	n/a	n/a
17	POLR2A	chr1:47901959-47902920	HCT-116	colon:	n/a	n/a
18	WRNIP1	chr1:47902134-47902749	GM12878	blood:	n/a	n/a
19	PML	chr1:47902037-47902695	GM12878	blood:	n/a	n/a
20	HNF4A	chr1:47902374-47902678	HepG2	liver:	n/a	chr1:47902552-47902565 chr1:47902552-47902567 chr1:47902553-47902565 chr1:47902552-47902565 chr1:47902551-47902566 chr1:47902548-47902570 chr1:47902552-47902566
21	TCF12	chr1:47902015-47902694	A549	lung:	n/a	chr1:47902311-47902321
22	CTCF	chr1:47902580-47902730	GM12873	blood:	n/a	n/a
23	POLR2A	chr1:47902066-47903914	Hela-S3	cervix:	n/a	n/a
24	HDAC2	chr1:47902202-47902801	HepG2	liver:	n/a	n/a
25	CHD1	chr1:47902593-47902789	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr1:47902080-47904090	HepG2	liver:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
27	CREB1	chr1:47902014-47904068	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:47902209-47903023	Hela-S3	cervix:	n/a	n/a
29	CCNT2	chr1:47902133-47904058	K562	blood:	n/a	chr1:47903693-47903702
30	CTCF	chr1:47902556-47902673	NHEK	skin:	n/a	chr1:47902578-47902591
31	MAZ	chr1:47901897-47903976	GM12878	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
32	POLR2A	chr1:47902171-47903941	NB4	blood:	n/a	n/a
33	CTCF	chr1:47902580-47902730	BE2_C	brain:	n/a	n/a
34	SIN3AK20	chr1:47902531-47904036	PANC-1	pancreas:	n/a	n/a
35	MYC	chr1:47902116-47903922	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
36	CTCF	chr1:47901795-47902870	HCT-116	colon:	n/a	chr1:47902578-47902591
37	CTCF	chr1:47902660-47902810	HMEC	breast:	n/a	n/a
38	HNF4A	chr1:47902292-47902717	HepG2	liver:	n/a	chr1:47902552-47902565 chr1:47902552-47902567 chr1:47902553-47902565 chr1:47902552-47902565 chr1:47902551-47902566 chr1:47902548-47902570 chr1:47902552-47902566
39	CTCF	chr1:47902496-47902698	GM12891	blood:	n/a	chr1:47902578-47902591
40	MYC	chr1:47902045-47903986	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
41	CTCF	chr1:47902548-47902677	Hela-S3	cervix:	n/a	chr1:47902578-47902591
42	CTCF	chr1:47902137-47902694	HepG2	liver:	n/a	chr1:47902578-47902591
43	HNF4G	chr1:47902372-47902705	HepG2	liver:	n/a	chr1:47902552-47902565 chr1:47902552-47902567 chr1:47902553-47902565 chr1:47902552-47902565 chr1:47902548-47902570 chr1:47902550-47902565 chr1:47902552-47902566
44	SMC3	chr1:47901894-47903047	SK-N-SH	brain:	n/a	chr1:47902581-47902591
45	ZNF384	chr1:47902163-47902759	K562	blood:	n/a	n/a
46	CHD2	chr1:47902174-47903867	Hela-S3	cervix:	n/a	chr1:47903702-47903712 chr1:47903380-47903390
47	POLR2A	chr1:47902665-47903009	HepG2	liver:	n/a	n/a
48	ZMIZ1	chr1:47902182-47902695	K562	blood:	n/a	n/a
49	POLR2A	chr1:47902456-47902796	GM12878	blood:	n/a	n/a
50	CEBPB	chr1:47902281-47902686	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47901774..47903783-chr1:47905502..47907193,2	MCF-7	breast:
2	chr1:47901790..47903824-chr1:48190200..48191775,2	K562	blood:
3	chr1:47902132..47902815-chr1:48175858..48176824,3	MCF-7	breast:
4	chr1:47902221..47904815-chr1:47929260..47931018,2	K562	blood:
5	chr1:47902573..47903219-chr14:100274224..100274724,2	Hela-S3	cervix:
6	chr1:47902455..47903363-chr10:89577216..89577997,2	Hela-S3	cervix:
7	chr1:47901999..47903599-chr1:48174794..48176429,2	MCF-7	breast:
8	chr1:47902477..47903371-chr9:131218074..131218707,2	Hela-S3	cervix:
9	chr1:47901910..47902768-chr1:48089857..48090558,2	K562	blood:
10	chr1:47902492..47903033-chr5:172194621..172195178,2	Hela-S3	cervix:
11	chr1:47902027..47902996-chr1:47935255..47935856,2	K562	blood:
12	chr1:47901842..47902786-chr1:48175848..48176467,3	K562	blood:

Variant related genes	Relation type
FOXD2-AS1	TF binding region
ENSG00000136811	Chromatin interaction
ENSG00000223820	Chromatin interaction
ENSG00000138138	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3432093	chr1:47901465-47906063	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv3406880	chr1:47901890-47905238	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:47901400-47902800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr1:47901600-47902800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr1:47901600-47902800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
6	chr1:47901800-47902800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:47901800-47902800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:47901800-47902800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
9	chr1:47901800-47903200	Flanking Active TSS	Liver	Liver
10	chr1:47901800-47903200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr1:47901800-47904000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr1:47901800-47904600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:47902000-47902800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:47902000-47902800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:47902000-47902800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:47902000-47902800	Flanking Active TSS	Colonic Mucosa	Colon
18	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr1:47902000-47902800	Bivalent Enhancer	Fetal Heart	heart
20	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
21	chr1:47902000-47902800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
22	chr1:47902000-47903000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:47902000-47903000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:47902000-47903200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr1:47902000-47903200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:47902000-47903200	Flanking Active TSS	HUVEC	blood vessel
27	chr1:47902000-47903600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:47902000-47904400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
29	chr1:47902000-47904400	Active TSS	A549	lung
30	chr1:47902000-47904800	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:47902200-47902800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
32	chr1:47902200-47902800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr1:47902200-47902800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
34	chr1:47902200-47902800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr1:47902200-47902800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:47902200-47902800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:47902200-47902800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
38	chr1:47902200-47902800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
39	chr1:47902200-47902800	Active TSS	Right Ventricle	heart
40	chr1:47902200-47902800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr1:47902200-47903000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
45	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr1:47902200-47903200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:47902200-47903200	Flanking Active TSS	Spleen	Spleen
48	chr1:47902200-47903600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr1:47902200-47904000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:47902200-47904000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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